Long non-coding RNAs as a source of new peptides

• Published in: eLife Vol. 3; p. e03523
• Main Authors: Ruiz-Orera, Jorge, Messeguer, Xavier, Subirana, Juan Antonio, Alba, M Mar
• Format: Journal Article Publication
• Language: English
• Published: England eLife Sciences Publications Ltd 16.09.2014; eLife Sciences Publications, Ltd
• Subjects: Amino acids; Animals; Aplicacions de la informàtica; Arabidopsis; Bioinformàtica; de novo gene evolution; Disease genes; Drosophila melanogaster; eukaryote; Evolution; Evolution, Molecular; Gene expression; Gene Expression Profiling; Genes; Genomics; Genomics and Evolutionary Biology; Human-cells; Humans; Informàtica; lncRNA; Medical informatics; Medicina; Mice; Open reading frames; Open Reading Frames - genetics; Peptides; Peptides - genetics; Polycistronic messenger-RNA; Protein Biosynthesis; Proteins; Proteomics; Reveals; ribosome profiling; Ribosomes; Ribosomes - genetics; Ribosomes - metabolism; RNA, Long Noncoding - genetics; RNA, Long Noncoding - metabolism; Saccaromyces-cerevisiae; Saccharomyces cerevisiae; Selection, Genetic; Sequence Analysis, RNA; Species Specificity; Transcriptional landscape; Zebrafish; Àrees temàtiques de la UPC; evolutionary biology; lncRNA; ribosome profiling; genomics; eukaryote; de novo gene evolution; human
• ISSN: 2050-084X; 2050-084X
• DOI: 10.7554/eLife.03523

Deep transcriptome sequencing has revealed the existence of many transcripts that lack long or conserved open reading frames (ORFs) and which have been termed long non-coding RNAs (lncRNAs). The vast majority of lncRNAs are lineage-specific and do not yet have a known function. In this study, we test the hypothesis that they may act as a repository for the synthesis of new peptides. We find that a large fraction of the lncRNAs expressed in cells from six different species is associated with ribosomes. The patterns of ribosome protection are consistent with the translation of short peptides. lncRNAs show similar coding potential and sequence constraints than evolutionary young protein coding sequences, indicating that they play an important role in de novo protein evolution. Despite the terms being largely interchangeable in modern language, ‘DNA’ and ‘gene’ do not mean the same thing. A gene is made of DNA and contains the instructions to make a protein, and it is the protein that performs the function of the gene. However, cells in the body also contain DNA that does not form genes. Far from being ‘junk’ DNA with no biological purpose; this DNA has a variety of roles, including affecting how other genes are used. To produce a protein, the DNA sequence of a gene is transcribed into an intermediate molecule called RNA, which is then translated to produce a protein. So-called long non-coding RNA (lncRNA) molecules are also transcribed from DNA, but whether these are translated to make proteins has been a subject of much debate. Indeed, the function of the vast majority of lncRNA molecules is unknown. Ruiz-Orera et al. analyzed RNA sequences collected from earlier experiments on six different species—humans, mice, fish, flies, yeast, and a plant—and found nearly 2500 as yet unstudied lncRNAs in addition to those previously identified. Many of the lncRNAs that Ruiz-Orera et al. investigated could be found lodged inside the cellular machinery used to translate RNA into proteins. Furthermore, these lncRNA molecules are oriented in the machinery as if they are primed and ready for translation, suggesting that many lncRNAs do produce proteins. However, it is unclear how many of these proteins have a useful function. Very few lncRNAs were found in more than one species, suggesting that they have evolved recently. The properties of lncRNA molecules also show many similarities with the properties of ‘young’—recently evolved—genes that are known to produce proteins. The combined findings of Ruiz-Orera et al. therefore suggest that lncRNAs are important for developing new proteins. The emergence of proteins with new functions has been an important driving force in evolution, and this work provides important clues into the first steps of this process.